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python2.7 sysconfig broken under virtualenv #118

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bukzor opened this Issue Apr 13, 2011 · 18 comments

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@bukzor

bukzor commented Apr 13, 2011

This is preventing numpy from installing correctly:

$ virtualenv --version
1.6

>>> import sysconfig
>>> sysconfig.get_config_vars()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/sysconfig.py", line 444, in get_config_vars
    _init_posix(_CONFIG_VARS)
  File "/usr/lib/python2.7/sysconfig.py", line 298, in _init_posix
    raise IOError(msg)
IOError: invalid Python installation: unable to open /home/bgolemon/software/sqlalchemy/local/lib/python2.7/config/Makefile (No such file or directory)

>>> sysconfig._get_makefile_filename()
'/home/bgolemon/software/sqlalchemy/local/lib/python2.7/config/Makefile'

Quick fix:
mkdir local
ln -s ../lib local/lib

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bukzor Apr 13, 2011

The culprit is this line at /usr/lib/python2.7/sysconfig.py:285

return os.path.join(get_path('stdlib').replace("/usr/local","/usr",1), "config" + (sys.pydebug and "_d" or ""), "Makefile")

There is no '/usr' in the stdlib path under virtualenv, so the string replace above doesn't do anything. I don't know whose bug this is really, or how best to fix it, so I'll leave it up to you all from here.

bukzor commented Apr 13, 2011

The culprit is this line at /usr/lib/python2.7/sysconfig.py:285

return os.path.join(get_path('stdlib').replace("/usr/local","/usr",1), "config" + (sys.pydebug and "_d" or ""), "Makefile")

There is no '/usr' in the stdlib path under virtualenv, so the string replace above doesn't do anything. I don't know whose bug this is really, or how best to fix it, so I'll leave it up to you all from here.

@bukzor bukzor closed this Apr 13, 2011

@bukzor bukzor reopened this Apr 13, 2011

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pshields May 22, 2011

I encountered this issue as well. The previous poster's quick fix worked for me as a temporary solution.

pshields commented May 22, 2011

I encountered this issue as well. The previous poster's quick fix worked for me as a temporary solution.

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scottza Jun 1, 2011

It looks like the function path_locations() in virtualenv.py needs to be special cased for Debian based systems with Python 2.7.

On my Ubuntu 11.04 machine

import sysconfig
print(sysconfig.get_paths())
{'platinclude': '/usr/local/include/python2.7', 'platstdlib': '/usr/local/lib/python2.7', 'platlib': '/usr/local/lib/python2.7/dist-packages', 'purelib': '/usr/local/lib/python2.7/dist-packages', 'stdlib': '/usr/local/lib/python2.7', 'scripts': '/usr/local/bin', 'include': '/usr/local/include/python2.7', 'data': '/usr/local'}

virtualenv puts stuff in $VIRTUAL_ENV/lib, $VIRTUAL_ENV/include etc.

My version of bukzor's workaround is:

Activate the virtualenv
mkdir $VIRTUAL_ENV/local
ln -s $VIRTUAL_ENV/lib $VIRTUAL_ENV/local/lib
Install Numpy

scottza commented Jun 1, 2011

It looks like the function path_locations() in virtualenv.py needs to be special cased for Debian based systems with Python 2.7.

On my Ubuntu 11.04 machine

import sysconfig
print(sysconfig.get_paths())
{'platinclude': '/usr/local/include/python2.7', 'platstdlib': '/usr/local/lib/python2.7', 'platlib': '/usr/local/lib/python2.7/dist-packages', 'purelib': '/usr/local/lib/python2.7/dist-packages', 'stdlib': '/usr/local/lib/python2.7', 'scripts': '/usr/local/bin', 'include': '/usr/local/include/python2.7', 'data': '/usr/local'}

virtualenv puts stuff in $VIRTUAL_ENV/lib, $VIRTUAL_ENV/include etc.

My version of bukzor's workaround is:

Activate the virtualenv
mkdir $VIRTUAL_ENV/local
ln -s $VIRTUAL_ENV/lib $VIRTUAL_ENV/local/lib
Install Numpy

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wgx731 Jun 8, 2011

I want to install numpy with virtualenv on Ubuntu 11.04 as well. Encounter error. This is my log:

Downloading/unpacking numpy
Running setup.py egg_info for package numpy
Running from numpy source directory./bin/sh: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/sse2
  libraries f77blas,cblas,atlas not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1417: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1426: UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1429: UserWarning:
    Blas (http://www.netlib.org/blas/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
  NOT AVAILABLE

/bin/sh: svnversion: not found
lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1333: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  libraries lapack not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack not found in /usr/local/lib
  libraries lapack not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1344: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1347: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE

build_src
building py_modules sources
building library "npymath" sources
error: None
Complete output from command python setup.py egg_info:
Running from numpy source directory./bin/sh: svnversion: not found

non-existing path in 'numpy/distutils': 'site.cfg'

F2PY Version 2

blas_opt_info:

blas_mkl_info:

libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries mkl,vml,guide not found in /usr/local/lib

libraries mkl,vml,guide not found in /usr/lib

NOT AVAILABLE

atlas_blas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2

libraries ptf77blas,ptcblas,atlas not found in /usr/lib

NOT AVAILABLE

atlas_blas_info:

libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries f77blas,cblas,atlas not found in /usr/local/lib

libraries f77blas,cblas,atlas not found in /usr/lib/sse2

libraries f77blas,cblas,atlas not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1417: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

blas_info:

libraries blas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries blas not found in /usr/local/lib

libraries blas not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1426: UserWarning:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

warnings.warn(BlasNotFoundError.doc)

blas_src_info:

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1429: UserWarning:

Blas (http://www.netlib.org/blas/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [blas_src]) or by setting

the BLAS_SRC environment variable.

warnings.warn(BlasSrcNotFoundError.doc)

NOT AVAILABLE

/bin/sh: svnversion: not found

lapack_opt_info:

lapack_mkl_info:

mkl_info:

libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries mkl,vml,guide not found in /usr/local/lib

libraries mkl,vml,guide not found in /usr/lib

NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2

libraries lapack_atlas not found in /usr/lib/sse2

libraries ptf77blas,ptcblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_threads_info

NOT AVAILABLE

atlas_info:

libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries f77blas,cblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib

libraries f77blas,cblas,atlas not found in /usr/lib/sse2

libraries lapack_atlas not found in /usr/lib/sse2

libraries f77blas,cblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_info

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1333: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

lapack_info:

libraries lapack not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack not found in /usr/local/lib

libraries lapack not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1344: UserWarning:

Lapack (http://www.netlib.org/lapack/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [lapack]) or by setting

the LAPACK environment variable.

warnings.warn(LapackNotFoundError.doc)

lapack_src_info:

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1347: UserWarning:

Lapack (http://www.netlib.org/lapack/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [lapack_src]) or by setting

the LAPACK_SRC environment variable.

warnings.warn(LapackSrcNotFoundError.doc)

NOT AVAILABLE

running egg_info

running build_src

build_src

building py_modules sources

building library "npymath" sources

error: None


Command python setup.py egg_info failed with error code 1

I have tried scottza's solution, but it doesn't work for me.
Any way to fix this? Thx

wgx731 commented Jun 8, 2011

I want to install numpy with virtualenv on Ubuntu 11.04 as well. Encounter error. This is my log:

Downloading/unpacking numpy
Running setup.py egg_info for package numpy
Running from numpy source directory./bin/sh: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/sse2
  libraries f77blas,cblas,atlas not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1417: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1426: UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1429: UserWarning:
    Blas (http://www.netlib.org/blas/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
  NOT AVAILABLE

/bin/sh: svnversion: not found
lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1333: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  libraries lapack not found in /home/wgx731/.virtualenvs/python2.7/lib
  libraries lapack not found in /usr/local/lib
  libraries lapack not found in /usr/lib
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1344: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1347: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE

build_src
building py_modules sources
building library "npymath" sources
error: None
Complete output from command python setup.py egg_info:
Running from numpy source directory./bin/sh: svnversion: not found

non-existing path in 'numpy/distutils': 'site.cfg'

F2PY Version 2

blas_opt_info:

blas_mkl_info:

libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries mkl,vml,guide not found in /usr/local/lib

libraries mkl,vml,guide not found in /usr/lib

NOT AVAILABLE

atlas_blas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2

libraries ptf77blas,ptcblas,atlas not found in /usr/lib

NOT AVAILABLE

atlas_blas_info:

libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries f77blas,cblas,atlas not found in /usr/local/lib

libraries f77blas,cblas,atlas not found in /usr/lib/sse2

libraries f77blas,cblas,atlas not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1417: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

blas_info:

libraries blas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries blas not found in /usr/local/lib

libraries blas not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1426: UserWarning:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

warnings.warn(BlasNotFoundError.doc)

blas_src_info:

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1429: UserWarning:

Blas (http://www.netlib.org/blas/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [blas_src]) or by setting

the BLAS_SRC environment variable.

warnings.warn(BlasSrcNotFoundError.doc)

NOT AVAILABLE

/bin/sh: svnversion: not found

lapack_opt_info:

lapack_mkl_info:

mkl_info:

libraries mkl,vml,guide not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries mkl,vml,guide not found in /usr/local/lib

libraries mkl,vml,guide not found in /usr/lib

NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2

libraries lapack_atlas not found in /usr/lib/sse2

libraries ptf77blas,ptcblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_threads_info

NOT AVAILABLE

atlas_info:

libraries f77blas,cblas,atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack_atlas not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries f77blas,cblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib

libraries f77blas,cblas,atlas not found in /usr/lib/sse2

libraries lapack_atlas not found in /usr/lib/sse2

libraries f77blas,cblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_info

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1333: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

lapack_info:

libraries lapack not found in /home/wgx731/.virtualenvs/python2.7/lib

libraries lapack not found in /usr/local/lib

libraries lapack not found in /usr/lib

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1344: UserWarning:

Lapack (http://www.netlib.org/lapack/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [lapack]) or by setting

the LAPACK environment variable.

warnings.warn(LapackNotFoundError.doc)

lapack_src_info:

NOT AVAILABLE

/home/wgx731/.virtualenvs/python2.7/build/numpy/numpy/distutils/system_info.py:1347: UserWarning:

Lapack (http://www.netlib.org/lapack/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [lapack_src]) or by setting

the LAPACK_SRC environment variable.

warnings.warn(LapackSrcNotFoundError.doc)

NOT AVAILABLE

running egg_info

running build_src

build_src

building py_modules sources

building library "npymath" sources

error: None


Command python setup.py egg_info failed with error code 1

I have tried scottza's solution, but it doesn't work for me.
Any way to fix this? Thx

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pnasrat Jun 8, 2011

Contributor

Thanks, for the update. We're aware of this issue and I hope to look at in more depth this weekend.

Contributor

pnasrat commented Jun 8, 2011

Thanks, for the update. We're aware of this issue and I hope to look at in more depth this weekend.

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flaviovdf Jun 25, 2011

Managed to get it working with the following workaround:

mkdir $VIRTUAL_ENV/local
ln -s $VIRTUAL_ENV/lib $VIRTUAL_ENV/local/lib
ln -s $VIRTUAL_ENV/include $VIRTUAL_ENV/local/include

flaviovdf commented Jun 25, 2011

Managed to get it working with the following workaround:

mkdir $VIRTUAL_ENV/local
ln -s $VIRTUAL_ENV/lib $VIRTUAL_ENV/local/lib
ln -s $VIRTUAL_ENV/include $VIRTUAL_ENV/local/include

@jezdez jezdez closed this in 285679c Jul 16, 2011

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robertmuil Mar 15, 2012

This fix is broken in certain setups.

If the python virtualenv path includes ...usr/local... then the virtualenv setup script will erroneously 'correct' it to ...local...

So, moving the virtualenv will avoid the problem: worth knowing for anyone who likes to install things under $HOME/usr.

robertmuil commented Mar 15, 2012

This fix is broken in certain setups.

If the python virtualenv path includes ...usr/local... then the virtualenv setup script will erroneously 'correct' it to ...local...

So, moving the virtualenv will avoid the problem: worth knowing for anyone who likes to install things under $HOME/usr.

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mikofski Apr 2, 2012

still can't install numpy under virtualenv, but I also couldn't install it with pip just in system env.
virtualenv 1.6.4
ubuntu 11.10
pip 1.0
distribute 0.6.16

mikofski commented Apr 2, 2012

still can't install numpy under virtualenv, but I also couldn't install it with pip just in system env.
virtualenv 1.6.4
ubuntu 11.10
pip 1.0
distribute 0.6.16

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dmckean Aug 17, 2013

Something in sysconfig in python 2.7 seems to be at fault.

Python 2.7.3 (default, Apr 10 2013, 06:20:15)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sysconfig
>>> sysconfig.get_config_vars()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/sysconfig.py", line 476, in get_config_vars
    _init_posix(_CONFIG_VARS)
  File "/usr/lib/python2.7/sysconfig.py", line 344, in _init_posix
    raise IOError(msg)
IOError: invalid Python installation: unable to open /usr/django/app/my_env/lib/python2.7/config/Makefile (No such file or directory)
>>> sysconfig.get_config_vars()
{'py_version_nodot': '27', 'exec_prefix': '/usr/local/django/app/my_env', 'platbase': '/usr/local/django/app/my_env', 'py_version_short': '2.7', 'prefix': '/usr/local/django/app/my_env', 'base': '/usr/local/django/app/my_env', 'projectbase': '/usr/local/django/app/my_env/bin', 'py_version': '2.7.3'}
>>>

dmckean commented Aug 17, 2013

Something in sysconfig in python 2.7 seems to be at fault.

Python 2.7.3 (default, Apr 10 2013, 06:20:15)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sysconfig
>>> sysconfig.get_config_vars()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/sysconfig.py", line 476, in get_config_vars
    _init_posix(_CONFIG_VARS)
  File "/usr/lib/python2.7/sysconfig.py", line 344, in _init_posix
    raise IOError(msg)
IOError: invalid Python installation: unable to open /usr/django/app/my_env/lib/python2.7/config/Makefile (No such file or directory)
>>> sysconfig.get_config_vars()
{'py_version_nodot': '27', 'exec_prefix': '/usr/local/django/app/my_env', 'platbase': '/usr/local/django/app/my_env', 'py_version_short': '2.7', 'prefix': '/usr/local/django/app/my_env', 'base': '/usr/local/django/app/my_env', 'projectbase': '/usr/local/django/app/my_env/bin', 'py_version': '2.7.3'}
>>>
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nicksloan Oct 18, 2013

This issue is caused by a patch applied by Ubuntu that specifically replaced /usr/local with /usr in several functions. Line 63404 in https://launchpadlibrarian.net/151545955/python2.7_2.7.3-5ubuntu4.3.diff.gz.

This stinks of taking a shortcut to support Ubuntu's deviations from the typical posix_local schema. Annoying.

For future reference: moving your virtualenv out of /usr/local... will fix it.

nicksloan commented Oct 18, 2013

This issue is caused by a patch applied by Ubuntu that specifically replaced /usr/local with /usr in several functions. Line 63404 in https://launchpadlibrarian.net/151545955/python2.7_2.7.3-5ubuntu4.3.diff.gz.

This stinks of taking a shortcut to support Ubuntu's deviations from the typical posix_local schema. Annoying.

For future reference: moving your virtualenv out of /usr/local... will fix it.

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brianz Nov 21, 2013

Hit this on Ubunu 12.04 and pip 1.4.1, virtualenv 1.10.1....moving the virtualenv out of /usr/local did the trick.

brianz commented Nov 21, 2013

Hit this on Ubunu 12.04 and pip 1.4.1, virtualenv 1.10.1....moving the virtualenv out of /usr/local did the trick.

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Neetuj Apr 25, 2014

running into the same issue
root@njain2:/usr/local/horizon# pip --version
pip 1.5.4 from /usr/local/lib/python2.7/dist-packages (python 2.7)
root@njain2:/usr/local/horizon# python --version
Python 2.7.3
root@njain2:/usr/local/horizon# virtualenv --version
1.7.1.2

File "/usr/lib/python2.7/sysconfig.py", line 344, in _init_posix

raise IOError(msg)
IOError: invalid Python installation: unable to open /usr/horizon/.venv/lib/python2.7/config/Makefile (No such file or directory)

Cleaning up...
Command python setup.py egg_info failed with error code 1 in /usr/local/horizon/.venv/build/cryptography
Storing debug log for failure in /root/.pip/pip.log

Neetuj commented Apr 25, 2014

running into the same issue
root@njain2:/usr/local/horizon# pip --version
pip 1.5.4 from /usr/local/lib/python2.7/dist-packages (python 2.7)
root@njain2:/usr/local/horizon# python --version
Python 2.7.3
root@njain2:/usr/local/horizon# virtualenv --version
1.7.1.2

File "/usr/lib/python2.7/sysconfig.py", line 344, in _init_posix

raise IOError(msg)
IOError: invalid Python installation: unable to open /usr/horizon/.venv/lib/python2.7/config/Makefile (No such file or directory)

Cleaning up...
Command python setup.py egg_info failed with error code 1 in /usr/local/horizon/.venv/build/cryptography
Storing debug log for failure in /root/.pip/pip.log

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Neetuj Apr 25, 2014

the file exists in /usr/local ..but i am not sure how to make it read from there .. and where exaclty it should be

root@njain2:/usr/local/horizon# ls /usr/horizon/.venv/lib/python2.7/config/Makefile
ls: cannot access /usr/horizon/.venv/lib/python2.7/config/Makefile: No such file or directory
root@njain2:/usr/local/horizon# ls /usr/local/horizon/.venv/lib/python2.7/config/Makefile
/usr/local/horizon/.venv/lib/python2.7/config/Makefile

Neetuj commented Apr 25, 2014

the file exists in /usr/local ..but i am not sure how to make it read from there .. and where exaclty it should be

root@njain2:/usr/local/horizon# ls /usr/horizon/.venv/lib/python2.7/config/Makefile
ls: cannot access /usr/horizon/.venv/lib/python2.7/config/Makefile: No such file or directory
root@njain2:/usr/local/horizon# ls /usr/local/horizon/.venv/lib/python2.7/config/Makefile
/usr/local/horizon/.venv/lib/python2.7/config/Makefile

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pkpp1233 Jul 11, 2014

i'm running into this same issue trying to install numpy in a docker container.

pkpp1233 commented Jul 11, 2014

i'm running into this same issue trying to install numpy in a docker container.

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bukzor Nov 14, 2014

@Neetuj: The culprit for you is still this line at /usr/lib/python2.7/sysconfig.py:285, shown above, although for a different reason.

bukzor commented Nov 14, 2014

@Neetuj: The culprit for you is still this line at /usr/lib/python2.7/sysconfig.py:285, shown above, although for a different reason.

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bukzor Nov 14, 2014

This was apparently an ill-conceived patch released by ubuntu for precise:
http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/precise/python2.7/precise-security/view/head:/debian/patches/distutils-install-layout.diff#L282

The replace statement is gone in trusty, but the scheme is still set to 'posix-local', so virtualenv's workaround persists, causing bugs in the coveragepy test suite under ubuntu:

https://bitbucket.org/ned/coveragepy/issue/337/test-failures-on-tip#comment-13653960

bukzor commented Nov 14, 2014

This was apparently an ill-conceived patch released by ubuntu for precise:
http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/precise/python2.7/precise-security/view/head:/debian/patches/distutils-install-layout.diff#L282

The replace statement is gone in trusty, but the scheme is still set to 'posix-local', so virtualenv's workaround persists, causing bugs in the coveragepy test suite under ubuntu:

https://bitbucket.org/ned/coveragepy/issue/337/test-failures-on-tip#comment-13653960

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naarkhoo Nov 25, 2014

I have the same problem - for installing Pilow on virtualenv

creating pip-egg-info/Pillow.egg-info

writing pip-egg-info/Pillow.egg-info/PKG-INFO

writing top-level names to pip-egg-info/Pillow.egg-info/top_level.txt

writing dependency_links to pip-egg-info/Pillow.egg-info/dependency_links.txt

writing manifest file 'pip-egg-info/Pillow.egg-info/SOURCES.txt'

warning: manifest_maker: standard file '-c' not found

error: invalid Python installation: unable to open /usr/lib/python2.7/config/Makefile (No such file or directory)


Cleaning up...
Command python setup.py egg_info failed with error code 1 in /home/rostam/.virtualenvs/myPelican/build/Pillow
Storing debug log for failure in /home/rostam/.pip/pip.log

Is there any workaround ?

naarkhoo commented Nov 25, 2014

I have the same problem - for installing Pilow on virtualenv

creating pip-egg-info/Pillow.egg-info

writing pip-egg-info/Pillow.egg-info/PKG-INFO

writing top-level names to pip-egg-info/Pillow.egg-info/top_level.txt

writing dependency_links to pip-egg-info/Pillow.egg-info/dependency_links.txt

writing manifest file 'pip-egg-info/Pillow.egg-info/SOURCES.txt'

warning: manifest_maker: standard file '-c' not found

error: invalid Python installation: unable to open /usr/lib/python2.7/config/Makefile (No such file or directory)


Cleaning up...
Command python setup.py egg_info failed with error code 1 in /home/rostam/.virtualenvs/myPelican/build/Pillow
Storing debug log for failure in /home/rostam/.pip/pip.log

Is there any workaround ?

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